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Localized reconstruction of Hepatitis B virus surface antigen dimer in the subviral particle with D2 symmetry from dataset A0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8YMJ
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.387 f_angle_d 0.803 f_chiral_restr 0.046 f_plane_restr 0.006 f_bond_d 0.004
Sample Hepatitis B virus ayw/China/Tibet127/2002
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 2864087 Reported Resolution (Å) 3.7 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (8YMJ) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 60
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1200 Maximum Defocus (nm) 1800 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 22500 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION RELION 3.1 IMAGE ACQUISITION SerialEM CTF CORRECTION CTFFIND 4 MODEL FITTING UCSF Chimera 1.16 INITIAL EULER ASSIGNMENT RELION 3.1 FINAL EULER ASSIGNMENT cryoSPARC 2.15 RECONSTRUCTION cryoSPARC 2.15 MODEL REFINEMENT PHENIX 1.20.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 10324877